Package org.strbio.mol.lib

These classes represent conceptual objects used in structural biology algorithms.

See:
Description

Interface Summary

AlignmentDependent	Interface for scoring functions that are dependent on the rest of the alignment.
Blast	Interface for common Blast-related routines.
GapModel	Interface for gap penalties for alignment.
PSIBlast	Interface for common PSI-blast related routines.
ScoreFunction	Interface for scoring functions.
ScoreSetup	Interface for scoring functions that need to be set up before being used on a given polymer.
ScoreSetup2	Interface for scoring functions that need to be set up before being used on a given seq/fold pair.
SSPredictor	Interface for common secondary structure prediction routines.
ThreadMethod	A method that does threading.

Class Summary

AlignmentParameters	Alignment parameters.
AlignmentParametersEA	Parameters, with some statistical functions to tell you how accurate they are at alignment and/or fold recognition.
BackbonePotential	methods for handling the 2ary prediction dependent backbone pseudopotential.
BlastAdapter	Adapter class to implement the routines in Blast.
BlastConstants	Some constants used in BLAST 2.0.6.
DayhoffMatrices	Dayhoff matrices (various) Dayhoff, MO 1978 Atlas of Protein Sequence and Structure volume 5, #3 p. 353 - 358.
FoldLibrary	A standard fold library for threading; i.e. the TOM fold library, or the Fischer fold library.
FRParameters	Fold recognition parameters.
FRParametersNode	Fold recognition parameters.
GapAffine	Affine gap penalties.
GapConstant	Constant gap penalties.
GapDistanceDependent	Distance dependent gap penalties.
GapModelAdapter	Default implementation of GapModel.
JMCThreadMethod	JMC's global threading method.
JMCThreadMethod2	JMC's global threading method, based on a combination of methods.
MinareaResults	Class containing results of minarea.
OptimalAAParameters	The optimal alignment parameters for maximizing alignment accuracy.
OptimalAAParametersFR	The optimal fold recognition parameters.
OptimalFRParameters	The optimal fold recognition parameters.
Pred2ary	Predicts secondary structure using JMC's Pred2ary program.
ProteinFilter	A file filter for returning likely protein formats.
PSIBlastMatrices	Matrix used in PSIBlast comparisons.
Score2ary	A scoring function that checks if the real 2ary structure matches.
ScoreAlphaTau	A scoring function that uses the 2ary prediction pseudopotential and alpha/tau angles of the fold.
ScoreAveragePSIBlast	A scoring function that uses PSI-BLAST matrices, averaging the score over all residues in the fold.
ScoreAverageReversePSIBlast	A scoring function that uses PSI-BLAST matrices.
ScoreBlosum62	A scoring function that uses the default Blosum62 matrix Version 1.0, 1/28/99 - original version
ScoreDefay	A scoring function from Tom Defay's algorithm.
ScoreFischer	A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold, while weighting a match by the predicted frequency.
ScoreID	A scoring function that returns a non-scaled identity matrix.
ScoreJDB10	A scoring function that uses JDB's 10% ID matrix.
ScoreList	A scoring function return a identity matrix; this is set up so that a sampling of all calls to score() over a large set of sequences and folds will average 0.0 with a standard deviation of 1.0.
ScorePairwiseDistance	A scoring function based on the CA distance between 2 residues.
ScorePhiPsi	A scoring function that uses the 2ary prediction pseudopotential and phi/psi angles of the fold.
ScorePred2ary	A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold.
ScorePredFreq	A scoring function that checks if the predicted 2ary structure in the sequence matches the real secondary structure in the fold, while weighting things by the predicted frequencies.
ScorePSIBlast	A scoring function that uses PSI-BLAST matrices.
ScoreReversePSIBlast	A scoring function that uses PSI-BLAST matrices.
ScoreScaledDefay	A scoring function from Tom Defay's algorithm, but rescaled.
ScoreScaledID	A scoring function that returns a scaled identity matrix.
ScoreSippl90	A scoring function that uses Sippl's 90 parameters, with the frozen approximation.
ScoreUFSippl90	A scoring function that uses Sippl's 90 parameters, without the frozen approximation.
Sippl90	Sippl scoring method, from JMB 90 papers.
ThreadResults	Threading results on one protein.
TOMFoldLibrary	The TOM fold library.
UserFoldLibrary	A standard fold library for threading, loaded in by the user.

Package org.strbio.mol.lib Description

These classes represent conceptual objects used in structural biology algorithms.